Question: Substitution Models For Download?
2
gravatar for dani.boobyer
7.9 years ago by
dani.boobyer40
St Andrews
dani.boobyer40 wrote:

Hi,

I need to add some substitution models into PAML (e.g. BLOSUM62, RtREV, VT). Is there anywhere I can download these from, ideally in .dat format?

Thanks for your help. Dani.

modeling paml • 2.9k views
ADD COMMENTlink modified 7.1 years ago by bilouorama0 • written 7.9 years ago by dani.boobyer40
2
gravatar for aravind ramesh
7.9 years ago by
India
aravind ramesh530 wrote:

Hai Dani,

1) For PAM250 2 For BLOSUM62 3) For Rt REV Matrices 4) For VT Matrices 5) A very good article regarding substitutional Matrices

Hope this helps

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by aravind ramesh530
1
gravatar for Woa
7.9 years ago by
Woa2.8k
United States
Woa2.8k wrote:

There was an issue with BLOSUM 62. Be sure you get the 'correct' BLOSUM series of substitution tables

ADD COMMENTlink written 7.9 years ago by Woa2.8k
0
gravatar for bilouorama
7.1 years ago by
bilouorama0
bilouorama0 wrote:

You can try this web site : http://www.genome.jp/aaindex/ You'll find about 90 substitution matrices with the publication related. It's an old resource but still full of many references.

ADD COMMENTlink written 7.1 years ago by bilouorama0
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